Re: [AMBER] velocity trajectory output

From: Daniel Roe <>
Date: Tue, 20 Jul 2021 11:41:06 -0400


On Mon, Jul 19, 2021 at 3:54 PM Daniel Konstantinovsky
<> wrote:
> I need accurate velocities to calculate correlation functions. I was
> wondering if the velocities written by sander and pmemd take periodic
> boundary conditions into account. For example, if a molecule jumps from one
> end of the box to the other end because of PBC over an MD step, does the
> corresponding velocity include the artifact of jumping across the box in
> one step or is that excluded? In other words, does the velocity trajectory
> include ridiculously large velocities due to wrapping? If yes, is there a

No. Coordinate wrapping (from iwrap=1) only affects the coordinates
that are written to trajectory/restart files. Internally, the
coordinates are not modified. So iwrap does not affect velocities (or
forces). If you see otherwise, definitely let us know, that would be a


> way to turn that off?
> Thank you!
> Daniel Konstantinovsky
> _______________________________________________
> AMBER mailing list

AMBER mailing list
Received on Tue Jul 20 2021 - 09:00:02 PDT
Custom Search